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JAXBElement<AnalysisType>}
AnalysisSet
AnalysisType
AnalysisType.ANALYSISATTRIBUTES
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
AnalysisType.ANALYSISFILES
AnalysisType.ANALYSISFILES.FILE
AnalysisType.ANALYSISLINKS
AnalysisType.ANALYSISLINKS.ANALYSISLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
AnalysisType.ANALYSISTYPE
AnalysisType.PARENT
AnalysisType.PARENT.EXPERIMENTREF
AnalysisType.PARENT.RUNREF
AnalysisType.PARENT.SAMPLEPOOLREF
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
AnalysisType.PARENT.SAMPLEREF
AnalysisType.PARENT.STUDYREF
JAXBElement<ExperimentType>}
ExperimentSet
ExperimentType
ExperimentType.DESIGN
ExperimentType.DESIGN.LIBRARYDESCRIPTOR
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
ExperimentType.DESIGN.SAMPLEDESCRIPTOR
ExperimentType.DESIGN.SPOTDESCRIPTOR
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
ExperimentType.EXPERIMENTATTRIBUTES
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
ExperimentType.EXPERIMENTLINKS
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
ExperimentType.PLATFORM
ExperimentType.PLATFORM.ABISOLID
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
ExperimentType.PLATFORM.HELICOS
ExperimentType.PLATFORM.ILLUMINA
ExperimentType.PLATFORM.LS454
ExperimentType.PROCESSING
ExperimentType.PROCESSING.BASECALLS
ExperimentType.PROCESSING.QUALITYSCORES
ExperimentType.STUDYREF
JAXBElement<RunType>}
RunSet
RunType
RunType.DATABLOCK
RunType.DATABLOCK.FILES
RunType.DATABLOCK.FILES.FILE
RunType.EXPERIMENTREF
RunType.RUNATTRIBUTES
RunType.RUNATTRIBUTES.RUNATTRIBUTE
RunType.RUNLINKS
RunType.RUNLINKS.RUNLINK
RunType.RUNLINKS.RUNLINK.ENTREZLINK
RunType.RUNLINKS.RUNLINK.URLLINK
JAXBElement<SampleType>}
SampleSet
SampleType
SampleType.MEMBERS
SampleType.MEMBERS.MEMBER
SampleType.SAMPLEATTRIBUTES
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
SampleType.SAMPLELINKS
SampleType.SAMPLELINKS.SAMPLELINK
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
SampleType.SAMPLENAME
JAXBElement<StudyType>}
StudySet
StudyType
StudyType.DESCRIPTOR
JAXBElement<String>}
StudyType.DESCRIPTOR.STUDYTYPE
StudyType.STUDYATTRIBUTES
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
StudyType.STUDYLINKS
StudyType.STUDYLINKS.STUDYLINK
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
StudyType.STUDYLINKS.STUDYLINK.URLLINK
JAXBElement<SubmissionType>}
SubmissionSet
SubmissionType
SubmissionType.ACTIONS
SubmissionType.ACTIONS.ACTION
SubmissionType.ACTIONS.ACTION.ADD
SubmissionType.ACTIONS.ACTION.HOLD
SubmissionType.ACTIONS.ACTION.MODIFY
SubmissionType.ACTIONS.ACTION.RELEASE
SubmissionType.ACTIONS.ACTION.SUPPRESS
SubmissionType.ACTIONS.ACTION.VALIDATE
SubmissionType.CONTACTS
SubmissionType.CONTACTS.CONTACT
SubmissionType.FILES
SubmissionType.FILES.FILE
Category.debug(Object).
Category.debug(Object,Throwable).
Category.error(Object).
Category.error(Object,Throwable).
Category.fatal(Object).
Category.fatal(Object,Throwable).
ValidationReportService.fileLinkReport(List) including all files in the SeqWare
meta db.
Category.info(Object).
Category.info(Object,Throwable).
Syntax:
./SNVMix2 -m [-i ] [-o ] [-T | -C | -F] [-p < q | m | s >] [-t < mb | m | b | M | Mb | MB | SNVMix1>] [-q <#>] [-Q <#>] [-a/-b/-d <#,#,#>] [-M ] [-h]
Required:
-m model file, a line for mu and a line for pi, three
space-separated values each, like:
mu 0.xxxxxxxx 0.xxxxxxxx 0.xxxxxxxx
pi 0.xxxxxxxx 0.xxxxxxxx 0.xxxxxxxx
Optional:
-i quality pileup, from pileup2matlab.pl script (def: STDIN)
-o where to put the results (def: STDOUT)
-T | -C | -F Train, Classify or Filter (def: Classify)
-p q|m|s Input pileup format (def: s)
q = quality
m = MAQ
s = SAMtools
-t mb|m|b|M|Mb|MB|SNVMix1
Filter type (def: mb)
mb Lowest between map and base quality
m Filter on map, and use as surrogate for base quality
b Filter on base quality, take map quality as 1
M Filter on map quality but use only base quality
Mb Filter on map quality and use both map and base qualities
MB Filter on map quality AND base quality
SNVMix1 Filter on base quality and map quality, afterwards consider them perfect
-q # Cutoff Phred value for Base Quality, anything <= this value is ignored (def: Q19)
-Q # Cutoff Phred value for Map Quality, anything <= this value is ignored (def: Q19)
Training parameters:
-a #,#,# Provide alpha training parameters
-b #,#,# Provide beta training parameters
-d #,#,# Provide delta training parameters
-M Provide a file containing training parameters (will override -a, -b and -d)
Values are space-separated:
alpha # # #
beta # # #
delta # # #
-apply-filter
-perl-path Path to perl installation
-filter-path Path to the filter script
-threshold THRESHOLD is given, then SNVs will be reported when the selected probability exceeds this
-c [2|3] TYPE is the number of classes to consider
'2' considers only AA and {AB U BB} (default)
'3' considers AA, AB and BB
-h this message
Category.debug(Object).
Category.debug(Object,Throwable).
Category.warn(Object).
Category.warn(Object,Throwable).
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